Groups

CLARK Users

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Welcome to the Google Group dedicated for the CLARK users!
You will find news, and other posts related to the tool.

Any questions or a problem to share?

Please read out previous post/conversations, over the past years many users have contributed with important and interesting posts. If you see a similar issue was reported in the past weeks/months then use it to continue the conversation, otherwise feel free to submit a post.

Github page: rouni001/CLARK (github.com), Webpage of CLARK: http://clark.cs.ucr.edu

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7/11/19

New Release V1.2.6.1

Dear CLARK users: The script "makeSummaryTables.sh" for generating summary tables has been

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New Release V1.2.6.1

Dear CLARK users: The script "makeSummaryTables.sh" for generating summary tables has been

7/11/19

9/6/16

[README] [HOW TO REPORT A BUG/ERROR] A bug in the program? Please help and report it this way...

Dear CLARK users, First of all, please make sure to run CLARK according to its instructions provided

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[README] [HOW TO REPORT A BUG/ERROR] A bug in the program? Please help and report it this way...

Dear CLARK users, First of all, please make sure to run CLARK according to its instructions provided

9/6/16

5/20/24

CLARV1.3.0.0: New Version Available !

Hi CLARK Users, Version v1.3.0.0 is available for download! The new release includes: - Fixed error

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CLARV1.3.0.0: New Version Available !

Hi CLARK Users, Version v1.3.0.0 is available for download! The new release includes: - Fixed error

5/20/24

Olivia Or, Rachid2

12/27/23

error in running set_targets.sh

Hello olilili ! Thank you for reaching out. Have you been able to move forward or is this error still

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error in running set_targets.sh

Hello olilili ! Thank you for reaching out. Have you been able to move forward or is this error still

12/27/23

7/12/23

Mask References?

Hi, Just wondering whether masking references will influence results from Clark. Am currently

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Mask References?

Hi, Just wondering whether masking references will influence results from Clark. Am currently

7/12/23

Yun Shen, … Matt Heatley3

7/12/23

add configurability to .settings, .DBDirectory and .dbAccess

i'd second this. i'm currently trying to run the singularity version of clark but can't

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add configurability to .settings, .DBDirectory and .dbAccess

i'd second this. i'm currently trying to run the singularity version of clark but can't

7/12/23

Lolo Aboufoul, Rachid2

5/19/23

Interpreting makeSummary.sh Results

Hi Lolo, Could you explain what you mean ? Could you show here how you'd like the output to be

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Interpreting makeSummary.sh Results

Hi Lolo, Could you explain what you mean ? Could you show here how you'd like the output to be

5/19/23

Lolo Aboufoul, Rachid2

5/19/23

makeSummaryTables.sh not yielding proper results

Hi Lolo! Great news: It seems you got it working, given your next post! Thank you, Rachid On Friday,

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makeSummaryTables.sh not yielding proper results

Hi Lolo! Great news: It seems you got it working, given your next post! Thank you, Rachid On Friday,

5/19/23

Wen-Shyong Tzou, Rachid2

4/24/23

the distribution of kmer on a long read fasta file

Hello Wen-Shyong, The location of k-mers are not stored and printed out in the classification report.

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the distribution of kmer on a long read fasta file

Hello Wen-Shyong, The location of k-mers are not stored and printed out in the classification report.

4/24/23

4/29/22

CLARK detecting less number of viruses in metavirome dataset

To CLARK team, I am using CLARK to find the taxonomy of viruses in metavirome (SRR10281034) dataset.

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CLARK detecting less number of viruses in metavirome dataset

To CLARK team, I am using CLARK to find the taxonomy of viruses in metavirome (SRR10281034) dataset.

4/29/22

Andrea Spitaleri, Rachid5

3/18/21

clark stuck during db creation

Hi I tried 2. but it did not work. 1. yes (clean installation and etc ...) thanks! Il giorno domenica

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database_creation

clark stuck during db creation

Hi I tried 2. but it did not work. 1. yes (clean installation and etc ...) thanks! Il giorno domenica

3/18/21

3/12/21

[IMPORTANT] [READ ME] [ HOW TO REPORT AN ERROR, BUG, AND OTHER UNEXPECTED BEHAVIOR]

Dear CLARK users, This message is intended to help the users wanting to report any issue they

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[IMPORTANT] [READ ME] [ HOW TO REPORT AN ERROR, BUG, AND OTHER UNEXPECTED BEHAVIOR]

Dear CLARK users, This message is intended to help the users wanting to report any issue they

3/12/21

Jumana Yousef, Rachid2

3/12/21

Dear user, I am afraid I do have limited information. You should be able to run these 3 commands

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Dear user, I am afraid I do have limited information. You should be able to run these 3 commands

3/12/21

Melissa Gray, Rachid2

1/21/21

Process killed in Line 177 of CLARKSCV1.2.6.1/classify_metagenome.sh

Hello mgsj..., I am sorry to hear your program was killed. Please contact your helpdesk for your

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Process killed in Line 177 of CLARKSCV1.2.6.1/classify_metagenome.sh

Hello mgsj..., I am sorry to hear your program was killed. Please contact your helpdesk for your

1/21/21

11/15/20

Sharing the pre-built database

Hello folks, Would it possible for some of you to share your Clark DB since it takes long time to

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Sharing the pre-built database

Hello folks, Would it possible for some of you to share your Clark DB since it takes long time to

11/15/20

Domenico Giosa, Rachid2

10/30/20

Process Killed on a 320Gb RAM machine

Hello Domenico, It seems your job was terminated and did not encountered an error. Please contact

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Process Killed on a 320Gb RAM machine

Hello Domenico, It seems your job was terminated and did not encountered an error. Please contact

10/30/20

Szymon, Rachid2

10/3/20

Hi Szymon, Thank you for reporting this issue! This is not normal behavior. Let's see, when did

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Hi Szymon, Thank you for reporting this issue! This is not normal behavior. Let's see, when did

10/3/20

Fengqing Wang, Rachid4

8/24/20

failde run rhe script buidSpacedDB.sh

Dear Rachid, update:It's working now. Thanks All the best, Fengqing 在2020年8月17日星期一 UTC+2 下午10:38:

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failde run rhe script buidSpacedDB.sh

Dear Rachid, update:It's working now. Thanks All the best, Fengqing 在2020年8月17日星期一 UTC+2 下午10:38:

8/24/20

Gabriel Amorim, Rachid7

8/17/20

Database Creation

Hi, I imagined that could be the reason. If I may suggest, it would be nice to update the Software

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Database Creation

Hi, I imagined that could be the reason. If I may suggest, it would be nice to update the Software

8/17/20

Marisol Ortiz, Rachid7

6/25/20

classify_metagenomes unable to find DIR_DB

Hi Rachid, Is there anything that might trigger the "database not found" error besides the

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classify_metagenomes unable to find DIR_DB

Hi Rachid, Is there anything that might trigger the "database not found" error besides the

6/25/20

Rami Baghdan, Rachid4

6/11/20

Setting custom target database cannot execute binary file error.

Hi Rami, Please see my answers below. I believe this post can be closed. Thank you! On Wednesday,

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Setting custom target database cannot execute binary file error.

Hi Rami, Please see my answers below. I believe this post can be closed. Thank you! On Wednesday,

6/11/20

6/4/20

How to increase the target limits?

Hello Rachid, I read in your replies that these limits (65535 (2^16-1) in CLARK and CLARK-l, and

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How to increase the target limits?

Hello Rachid, I read in your replies that these limits (65535 (2^16-1) in CLARK and CLARK-l, and

6/4/20

You Me, Rachid2

4/8/20

extractSequences.sh on gzipped input files

Hi, As for today, this script accepts only fast/fastq files. Please go ahead and uncompress your file

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extractSequences.sh on gzipped input files

Hi, As for today, this script accepts only fast/fastq files. Please go ahead and uncompress your file

4/8/20

Nilay Lale, Rachid3

3/11/20

Database creation is taking more than 24 hours

Hi Nilay, I was wondering if you could provide some updates regarding the issue you encountered. Were

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Database creation is taking more than 24 hours

Hi Nilay, I was wondering if you could provide some updates regarding the issue you encountered. Were

3/11/20

kathirvel k, Rachid4

3/11/20

Struggling to download Databases

Hi Kathirvel, Have you been able to download the database from RefSeq? Thank you, Best, Rachid On

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Struggling to download Databases

Hi Kathirvel, Have you been able to download the database from RefSeq? Thank you, Best, Rachid On

3/11/20

kathirvel k, Rachid3

3/11/20

I have Downloaded Databases Bacteria Virus separately and Fungi separately. Is this will create problem ?

Hi Kathirvel, I am checking-in to see whether my answer addressed your question. Does it make sense?

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I have Downloaded Databases Bacteria Virus separately and Fungi separately. Is this will create problem ?

Hi Kathirvel, I am checking-in to see whether my answer addressed your question. Does it make sense?

3/11/20

Divya Inamdar, Rachid10

3/11/20

Error in the classify_metagenome.sh step from the README file

H Divya, Is this issue still happening to you? Could you share with us some updates? Thank you for

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Error in the classify_metagenome.sh step from the README file

H Divya, Is this issue still happening to you? Could you share with us some updates? Thank you for

3/11/20

Alexander Nagy, Rachid2

12/4/19

Hi Alexander! I have been running CLARK tools on various samples/datasets produced by ONT sequences.

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Hi Alexander! I have been running CLARK tools on various samples/datasets produced by ONT sequences.

12/4/19

Nilay Lale, Rachid2

11/29/19

Creating a bacterial DB is taking more than 24 hours

Hi Nilay, The command "set_targets.sh" does not build the databases but rather downloads

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Creating a bacterial DB is taking more than 24 hours

Hi Nilay, The command "set_targets.sh" does not build the databases but rather downloads

11/29/19

Jussi Volanen, … Rachid5

11/29/19

Creating 16S database really slow

Hi Owen, Yes, the source code is publicly available. As indicated in the CLARK peer-reviewed

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Creating 16S database really slow

Hi Owen, Yes, the source code is publicly available. As indicated in the CLARK peer-reviewed

11/29/19

marisol ortiz, Rachid6

10/18/19

makeSummary.sh not recognizing estimate_abundance.sh output

Yes. Anytime! On Friday, October 18, 2019 at 7:25:15 PM UTC-4, marisol ortiz wrote: Hi Rachid, so I

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makeSummary.sh not recognizing estimate_abundance.sh output

Yes. Anytime! On Friday, October 18, 2019 at 7:25:15 PM UTC-4, marisol ortiz wrote: Hi Rachid, so I

10/18/19

10/18/19

Problem running buildSpacedDB.sh

Hi Kate, Please let me know whether this answer helped? Thank you, Rachid On Tuesday, September 10,

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Problem running buildSpacedDB.sh

Hi Kate, Please let me know whether this answer helped? Thank you, Rachid On Tuesday, September 10,

10/18/19

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